Favorite things to see in Venice?

Torcello may be interesting if you wanted to revisit Murano and /or Burano. I've never visited San Michele Cemetery Island, but I've seen people mention it and seem to enjoy a visit.

Not sure how your teenage boys feel about Naval History, but there is a Naval Museum over by Arsenale. Now, I haven't been - we were going to go the last time in Venice but it closed before we got there.

If you want to do a bell tower view but don't want to wait in the long line at St Mark's Campanile, head across the lagoon to San Giorgio - prob won't be a line at all, and you have nice views over to St Mark's Sq.

For a maybe less well known church, Santa Maria Gloriosa dei Frari is lovely.

And if you haven't done the Doge's Palace - I'd say that's one of the top things to do.

A few off-the-beaten-path ideas:

1) Take rowing lessons. There is a non-profit group at rowvenice.org that teaches you how to row in the Venetian style. You will learn to how row a batello, which at first glance looks like a gondola but is a bit more stable. You will need to block off an afternoon to do it, but it is well worth it. It's one of the most educational and enjoyable things I have done in Venice --- and I have spent several weeks in Venice over the past couple of years.

2) Take mask painting lessons at Ca'Macana in Dorsuduro.

3) Musica a Palazzo performs opera in a 15th century palazzo. They have fine musicians and the setting is gorgeous. It may not be the best choice if you are traveling with teenage boys, though.

4) Do a cicchetti crawl one afternoon or evening. My favorite is Cantine del Vino Gia Schiavi in Dorsoduro

Torcello is good for a picnic, and you can climb the campanile, as the restoration is completed.

Thre are two naval museums, one essentially "naval", the other looks at general merchant vessels. Both are near the Arsenale, and kids would enjoy them. This 68 year old "kid" found them fascinating.

Venicekayak.com might be worh a look. Not sure if there are age limits, but we have paddled twice with them and it was great fun.

Check out the amazing view over Venice from the roof terrace at the Tedeschi(sp?) mall near the Rialto bridge

We just took our 2 teen girls and all really liked the rick steves vaporetto tour (slow boat with RS audio guide). This would be a good activity for first day zombie syndrome. The gondola ride was also a highlight! So peaceful!

The boys also might like the Doge's palace. The upstairs is a little underwhelming but there is also a tour of the prison which you get to by crossing over the bridge of sighs.

I agree that walking the streets is still one of the best things to do in Venice. Maybe put the boys in charge of navigating!?

Who doesn't fall in love with Venice walking out of the train station, with that big reveal!

We liked the Secret Itinerary tour of the Doge's Palace when we took our son. Great stories!

Maybe not sites/sights but things to do:
Stroll Guidecca, visit the Cipriani Hotel
Stroll St. Mark's at night
Stroll anywhere at 6am and watch the city come alive as the suppliers deliver their goods to the shops and restaurants
Have a Bellini at Harry's Bar (a sight in itself), have a spritzer with Campari (watch out here)
Take the lift in the campanile at St. Giorgio Maggiore for spectacular views of the city and no lines
Have or a drink in St. Marks at 8:20pm at one of the concert restaurants
Visit the Giardini della Biennale
Listen to Vivaldi somewhere, there are a lot of musical performances in churches during the evening and Vivaldi is a favorite son of Venenzia. Vivaldi's Four Seasons are playing somewhere in town.
Walk along the waterfront on the south side of Dorsoduro and watch the fisherman
Visit the Guggenheim and Accademia
Go to the casino Ca d'Oro, but wear a jacket
Have pizza at Da Mamo's, or better yet, branzino

That should take care of your two days.

I loved all of Venice and I think your "guys" would enjoy climbing to the top of the tower on St. Mark's Square. ( there is an elevator)
We went in the AM before any crowds and the views are amazing.

Guided tour of the clock tower in San Marco square.

If you are early risers (doubtful with teenaged boys :-) ) you could go to a Catholic Mass at the cathedral in the square and see it glow golden in the sunlight.